That's it! Thanks Alex.
I had a little trouble tracking down the file, wish this were better
documented. For anybody who discovers this later, I found it here
$ sudo find / -name "dev_appserver.datastore.history" -print
/private/var/folders/Mq/Mq6HCC1-F8enD-Rr+rKv2k+++TI/-Tmp-/
dev_appserver.d
Try removing the database access history file, then restarting the
development server. The file is called dev_appserver.datastore.history
and located in the tmp directory.
The development server auto-generates the indices based on the history
file, even if you don't run the corresponding queries